www.nature.com/scientificreports OPEN NT5C2 methylation regulatory interplay between DNMT1 and insulin receptor in type 2 diabetes Yng‑Tay Chen1*, Wei‑De Lin2,3, Wen‑Ling Liao4,5, Ya‑Ching Tsai2, Jiunn‑Wang Liao6 & Fuu‑Jen Tsai2,7,8* Epigenetics alternation of non‑genetic variation and genome‑wide association study proven allelic variants may associate with insulin secretion in type 2 diabetes (T2D) development. We analyzed promoter DNA methylation array to evaluate the associated with increased susceptibility to T2D (30 cases, 10 controls) and found 1,091 gene hypermethylated in promoter regions. We performed the association study of T2D and found 698 single nucleotide polymorphisms in exon and promoter sites by using 2,270 subjects (560 cases, 1,710 controls). A comparison of DNA hypermethylation and gene silencing of mouse T2D results in our T2D patients’ results showed that the 5′‑nucleotidase, cytosolic II (NT5C2) and fucosyltransferase 8 (FUT8) genes were strongly associated with increased susceptibility to T2D. DNA hypermethylation in promoter regions reduced NT5C2 gene expression, but not FUT8 in T2D patients. NT5C2 protein expression was decreased in pancreatic β‑cells from T2D mice. Transient transfection NT5C2 into RIN‑m5F cells down‑regulated DNA methyltransferase I (DNMT1) expression and up‑regulation of the insulin receptor. Moreover, NT5C2 knockdown induced in DNMT1 overexpression and insulin receptor inhibition. Taken together, these results showed that NT5C2 epigenetically regulated insulin receptor in patients and mice with T2D, and maybe provide for T2D therapy strategy. Te increasing prevalence of type 2 diabetes (T2D) is a global health problem. T2D can lead to various complica- tions, including diabetic nephropathy, retinopathy, stroke, neuropathy, atherosclerosis, and hypertension, afect- ing patient quality of life and mortality. T2D is a disease with multifactor whose onset and development depend on not only genetic factors but also other factors, for example, epigenetics regulations. Epigenetic mechanisms may play an important role in T2D development 1,2. T2D is characterized by hyperglycemia, pancreatic β-cell dys- function, decreased insulin signaling action, and increased hepatic glucose formation 3–5. In the pancreas, DNA methylation is involved in regulating de novo β-cell formation6. Previously studies have indicated that epigenetic factors conduce to the onset of T2D7–12. However, the mechanisms how DNA methyltransferase I (DNMT1) regulate T2D are unclear, and the roles of DNMT1 in T2D onset and development have not been clarifed. Investigation of the associations of DNA methylation in the peripheral blood may facilitate the identifcation of biomarkers for noninvasive early disease detection in epidemiological studies 13. DNA methylation, may be associated with regulation of the risk of many pathologies, such as T2D. DNA methylation can also afect the relationship between T2D and environmental exposure 14. Evaluation of epigenetics diference by Genome-wide DNA methylation arrays have become popular to assess disease progression. Currently, T2D onset and development biomarker identify from by epigenetics regulation still unclear in Taiwan Han Chinese. We using a DNA methylation array results to comparison with single nucleotide polymorphisms (SNPs) to looking for biomarker. Moreover, how DNMT1 afects the insulin signaling 1Graduate Institute of Food Safety, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan. 2Human Genetic Center, Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan. 3School of Post Baccalaureate Chinese Medicine, China Medical University, Taichung, Taiwan. 4Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan. 5Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan. 6Graduate Institute of Veterinary Pathobiology, National Chung Hsing University, Taichung, Taiwan. 7School of Chinese Medicine, China Medical University, Taichung, Taiwan. 8Department of Health and Nutrition Biotechnology, Asia University, Taichung, Taiwan. *email: [email protected]; [email protected] Scientifc Reports | (2020) 10:16087 | https://doi.org/10.1038/s41598-020-71336-9 1 Vol.:(0123456789) www.nature.com/scientificreports/ T2D Controls Number 30 10 Male/female (%) 50/50 50/50 Age at study (years) 61.9 ± 10.4 59.3 ± 8.8 BMI (kg/m2) 25.5 ± 4.6 23.5 ± 3.8 HbA1c (%) 8.4 ± 2.0 5.3 ± 0.6 Fasting plasma glucose (mg/dL) 141.4 ± 34.7 – Diabetic duration (years) 13.1 ± 3.9 – SBP (mmHg) 131.6 ± 18.4 128.8 ± 18.8 DBP (mmHg) 76.7 ± 11.6 75.5 ± 11.0 Table 1. Clinical characteristics of the subjects for DNA methylation array. T2D (N = 560) Control (N = 1,710) P* Male (%) 52.1 50 0.379 Age at study 63.2 ± 11.5 47.4 ± 10.7 < 0.001 Age at diagnosis 50.5 ± 13.1 – BMI (kg/m2) 25.7 ± 4.2 24.3 ± 3.6 < 0.001 HbA1c (%) 7.9 ± 1.8 5.8 ± 0.9 < 0.001 Fasting plasma glucose (mg/dL) 145.6 ± 66.5 96.3 ± 21.3 < 0.001 SBP (mmHg) 141.4 ± 19.7 113.8 ± 16.4 < 0.001 DBP (mmHg) 79.5 ± 13.3 71.8 ± 11.2 < 0.001 Table 2. Demographic and clinical characteristic for subjects who were used for identifed 698 SNPs. Values are presented as N (%) or mean ± SD. T2D type 2 diabetes, BMI body mass index, HbA1c hemoglobin A1c, SBP systolic blood pressure, DBP diastolic blood pressure. *P value for chi square test or two-sample independent t test. pathway, we examined epigenetic changes in patients with T2D, a mouse model of T2D, and in vitro transfec- tions experiences. Our results provided the important role of DNA methylation in the T2D disease pathway. Results DNA promoter methylation in patients with T2D. We performed a promoter DNA methylation array of samples from 30 patients with T2D and 10 healthy controls, and clinical characteristics of the subjects showed in Table 1. DNA methylation array data are accessible via the Gene Expression Omnibus (GEO) database, acces- sion number GSE81868 (https:// www. ncbi. nlm. nih. gov/ geo/ query/ acc. cgi? acc= GSE81 868). Analysis of DNA methylation status was carried out using model-based analysis of tiling-arrays (MAT) levels, found 1,091 genes were hypermethylation in promoter regions (Table S4). SNPs in T2D. We performed DNA promoter and exonic sites of susceptibility SNPs to T2D from subjects of 560 T2D cases and 1,710 controls, clinical characteristics of the subjects shown in Table 2. We found 698 SNPs at promoter and exon regions associated with T2D (Table S1). Tere are 33 genes not only with SNPs susceptibility to T2D but also DNA promoter hypermethylation (Table 3). DNA promoter hypermethylation and gene expression in T2D mice. We next performed pro- moter DNA methylation array analysis using KK-Ay mice with T2D and KK control mice. DNA methylation array data are accessible via the GEO database, accession number GSE100677 (https:// www. ncbi. nlm. nih. gov/ geo/ query/ acc. cgi? acc= GSE10 0677). Te primary data are accessible via the GEO database, accession number GSE101879 (https:// www. ncbi. nlm. nih. gov/ geo/ query/ acc. cgi? acc= GSE10 1879). We found 260 genes showing DNA promoter hyper-methylation and gene silencing (Table S2). Comparison of epigenetic changes in genes in humans and mice with T2D. We compared the 33 genes from human T2D to 260 genes from mice T2D. We identifed the 5′-nucleotidase, cytosolic II (NT5C2) and fucosyltransferase 8 (FUT8) genes which were associated with susceptibility to T2D not only SNPs but also DNA promoter hypermethylation in human T2D, and gene expression inhibition following by DNA methyla- tion in T2D model mice (Fig. 1). Te positions of NT5C2 and FUT8 SNPs were located on chr10:103089387 and chr14:65900969, respectively. NT5C2 and FUT8 DNA promoter methylation MAT-score were 5.13721 and 4.19785, respectively. Scientifc Reports | (2020) 10:16087 | https://doi.org/10.1038/s41598-020-71336-9 2 Vol:.(1234567890) www.nature.com/scientificreports/ Transcript ID Gene symbol MAT-score Description NM_199427 ZFP64 9.10027 ZFP64 zinc fnger protein NM_000814 GABRB3 8.33046 Gamma-aminobutyric acid type A receptor beta3 subunit NM_015335 MED13L 7.13939 Mediator complex subunit 13 like NM_001282773 RGS7 6.8489 Regulator of G-protein signaling 7 NM_006699 MAN1A2 5.49222 Mannosidase alpha class 1A member 2 NM_001289905 IL17RA 5.48686 Interleukin 17 receptor A NM_001401 LPAR1 5.20981 Lysophosphatidic acid receptor 1 NM_001035235 SRA1 5.17213 Steroid receptor RNA activator 1 NM_001134373 NT5C2 5.13721 5′-Nucleotidase, cytosolic II NM_001282225 CECR1 5.11905 Cat eye syndrome chromosome region candidate 1 NM_001258282 LINGO2 4.95801 Leucine rich repeat and Ig domain containing 2 NM_203349 SHC4 4.78135 Src homology 2 domain containing family member 4 NM_001286401 TMEM217 4.60762 Transmembrane protein 217 NM_001243042 HLA-C 4.46832 Major histocompatibility complex, class I, C NM_001102654 NTF3 4.45068 Neurotrophin 3 NR_033984 LOC400548 4.35767 Uncharacterized LOC400548 NM_001166412 SMOC2 4.33842 SPARC related modular calcium binding 2 NM_018429.2 BDP1 4.28144 B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB NM_004480 FUT8 4.19785 Fucosyltransferase 8 NM_182511 CBLN2 4.18523 Cerebellin 2 precursor NM_001243108 PLD2 4.17228 Phospholipase D2 NM_002318 LOXL2 4.13622 Lysyl oxidase like 2 NM_005215 DCC 4.11725 DCC netrin 1 receptor NM_001010848 NRG3 4.11385 Neuregulin 3 NM_001195001 PTPRU 4.08896 Protein tyrosine phosphatase, receptor type U NM_016529 ATP8A2 4.05786 ATPase phospholipid transporting 8A2 NM_002263 KIFC1 4.00384 Kinesin family member C1 NM_001105579 SYNDIG1L 3.93368 Synapse diferentiation inducing 1 like NM_001759 CCND2 3.78164 Cyclin D2 NM_001166058 RXFP2 3.71546 Relaxin/insulin like family peptide receptor 2 NM_022469 GREM2 3.69799 Gremlin 2, DAN family BMP antagonist NM_153810 CACUL1 3.55334 CDK2 associated Cullin domain 1 NM_001145159 INTS9 3.5282 Integrator complex subunit 9 Table 3. DNA methylation and SNP matching gene list in patients with T2D. NT5C2 and FUT8 mRNA expression from peripheral blood of T2D patients.